1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
|
# fmt: off
import numpy as np
import pytest
from ase.build import bulk
from ase.calculators.singlepoint import SinglePointDFTCalculator
from ase.io import read, write
magres_with_complex_labels = """#$magres-abinitio-v1.0
# Fictional test data
[atoms]
units lattice Angstrom
lattice 8.0 0.0 0.0 0.0 10.2 0.0 0.0 0.0 15.9
units atom Angstrom
atom H H1 1 3.70 4.9 1.07
atom H H2 100 4.30 2.1 5.15
atom H H2a 101 4.30 2.1 5.15
atom H H2b 102 4.30 2.1 5.15
[/atoms]
[magres]
units ms ppm
ms H1 1 3.0 -5.08 -3.19 -4.34 3.42 -3.78 1.05 -1.89 2.85
ms H2100 3.0 5.08 3.19 4.34 3.42 -3.78 -1.05 -1.89 2.85
ms H2a101 3.0 5.08 3.19 4.34 3.42 -3.78 -1.05 -1.89 2.85
ms H2b 102 3.0 5.08 3.19 4.34 3.42 -3.78 -1.05 -1.89 2.85
units efg au
efg H1 1 9.6 -3.43 1.45 -3.43 8.52 -1.43 1.45 -1.43 -1.81
efg H2100 9.6 3.43 -1.45 3.43 8.52 -1.43 -1.45 -1.43 -1.81
efg H2a101 9.6 3.43 -1.45 3.43 8.52 -1.43 -1.45 -1.43 -1.81
efg H2b 102 9.6 3.43 -1.45 3.43 8.52 -1.43 -1.45 -1.43 -1.81
[/magres]
"""
magres_with_too_large_index = """#$magres-abinitio-v1.0
# Test data with index >999
[atoms]
units lattice Angstrom
lattice 10.0 0.0 0.0 0.0 10.0 0.0 0.0 0.0 10.0
units atom Angstrom
atom H H1 1000 0.0 0.0 0.0
[/atoms]
[magres]
units ms ppm
ms H11000 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 1.0
[/magres]
"""
def test_magres():
# Test with fictional data
si2 = bulk('Si')
ms = np.ones((2, 3, 3))
si2.set_array('ms', ms)
efg = np.repeat([[[1, 0, 0], [0, 1, 0], [0, 0, -2]]], 2, axis=0)
si2.set_array('efg', efg)
calc = SinglePointDFTCalculator(si2)
calc.results['sus'] = np.eye(3) * 2
si2.calc = calc
si2.info['magres_units'] = {'ms': 'ppm',
'efg': 'au',
'sus': '10^-6.cm^3.mol^-1'}
write('si2_test.magres', si2)
si2 = read('si2_test.magres')
assert (np.trace(si2.get_array('ms')[0]) == 3)
assert (np.all(np.isclose(si2.get_array('efg')[:, 2, 2], -2)))
assert (np.all(np.isclose(si2.calc.results['sus'], np.eye(3) * 2)))
def test_magres_large(datadir):
# Test with big structure
assert len(read(datadir / "large_atoms.magres")) == 240
def test_magres_sitelabels(datadir):
"""Test reading magres files with munged site labels and indices
for cases where the site label has a number in it."""
# Write temporary file
with open('magres_with_complex_labels.magres', 'w') as f:
f.write(magres_with_complex_labels)
# Read it back
atoms = read('magres_with_complex_labels.magres')
labels_ref = ['H1', 'H2', 'H2a', 'H2b']
labels = atoms.get_array('labels')
np.testing.assert_array_equal(labels, labels_ref)
indices_ref = [1, 100, 101, 102]
indices = atoms.get_array('indices')
np.testing.assert_array_equal(indices, indices_ref)
def test_magres_with_large_indices():
"""Test handling of magres files with indices >999"""
# Write temporary file
with open('magres_large_index.magres', 'w') as f:
f.write(magres_with_too_large_index)
# Check that reading raises the correct error
with pytest.raises(RuntimeError, match="Index greater than 999 detected"):
read('magres_large_index.magres')
|
